  169  vi MESA_Exome_Aug2012_byidno_20130329.bim 
  170  sed 's/exm-rs/rs/g' MESA_Exome_Aug2012_byidno_20130329.bim|grep rs|head
  171  sed 's/exm-rs/rs/g' MESA_Exome_Aug2012_byidno_20130329.bim > MESA_Exome_Aug2012_byidno_20130329_tmp.bim
  172  mv MESA_Exome_Aug2012_byidno_20130329_tmp.bim MESA_Exome_Aug2012_byidno_20130329.bim
  173  vi MESA_Exome_Aug2012_byidno_20130329.bim
  174  vi perl_restrict_exome_mesa.pl
  175  ls ../../mesa6814_protein_race.csv 
  176  vi perl_restrict_exome_mesa.pl
  177  head ../../mesa6814_protein_race.csv
  178  vi perl_restrict_exome_mesa.pl
  179  perl perl_restrict_exome_mesa.pl
  180  vi perl_restrict_exome_mesa.pl
  181  perl perl_restrict_exome_mesa.pl
  182  wc -l MESA_Exome_Aug2012_byidno_20130329_final.txt 
  183  cat  perl_restrict_exome_mesa.pl
  184  ls
  185  plink --bfile MESA_Exome_Aug2012_byidno_20130329 --keep MESA_Exome_Aug2012_byidno_20130329_final.txt --make-bed --out MESA_Exome_Aug2012_byidno_20130329_final
  186  ls
  187  wc -l MESA_Exome_Aug2012_byidno_20130329_final.bim MESA_Exome_Aug2012_byidno_20130329_final.fam
  188  ls
  189  cd ..
  190  ls
  191  cd ..
  192  ls
  193  mkdir FINAL_MERGING
  194  cd FINAL_MERGING/
  195  ls
  196  mkdir CGPANEL
  197  mkdir IBC
  198  mkdir AFFY
  199  mkdir EXOME
  200  plink --bfile ../Exome/Plink_20130329/MESA_Exome_Aug2012_byidno_20130329_final --transpose --recode --out ./EXOME/Exome_final
  201  plink --bfile ../merge_IBC/Sample_mapping_merge_final --transpose --recode --out ./I
  202  ls
  203  wc -l ../merge_affy/extract_merge_final.fam ../merge_affy/merge_final.fam 
  204   plink --bfile ../merge_affy/extract_merge_final --transpose --recode --out ./AFFY/AFFY_final
  205   plink --bfile ../merge_affy/extract_merge_final --transpose --recode --out ./CGPANEL/CGPANEL_final
  206   plink --bfile ../CGPANEL12/SNPS2882 --transpose --recode --out ./CGPANEL/CGPANEL_final
  207  ls
  208  pwd
  209  cd IBC/
  210  ls
  211  perl /data4/bsi/bioinf_int/s106381.borawork/naresh_scripts/PAPER/ezimputer/Upgrade_inputmarkers_to_build37_by_DBSNP.pl 
  212  pwd
  213  ls ..
  214  cd ../CGPANEL/
  215  ls
  216  perl Upgrade_inputmarkers_to_build37_by_DBSNP.pl  -DBSNP_DIR /data4/bsi/bioinf_ext2/s109990/m081429_mesa/FINAL_MERGING/DB_DIR -DBSNP_DOWNLOADLINK ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606/database/organism_data/b137_SNPChrPosOnRef.bcp.gz  -INPUT_FILE /data4/bsi/bioinf_ext2/s109990/m081429_mesa/FINAL_MERGING/CGPANEL/CGPANEL_final.tped -REMAPPED_CURRENT_BUILD /data4/bsi/bioinf_ext2/s109990/m081429_mesa/FINAL_MERGING/CGPANEL/CGPANEL_final_build37.tped -NOTMAPPED_OLD_BUILD /data4/bsi/bioinf_ext2/s109990/m081429_mesa/FINAL_MERGING/CGPANEL/CGPANEL_final_build36.tped
  217  vi Upgrade_37.csh
  218  qsub Upgrade_37.csh
  219  cd ../IBC/
  220  cp ../CGPANEL/Upgrade_37.csh .
  221  ls
  222  vi Upgrade_37.csh 
  223  qsub Upgrade_37.csh 
  224  cd ../AFFY/
  225  cp ../IBC/Upgrade_37.csh .
  226  pwd
  227  ls
  228  vi Upgrade_37.csh 
  229  qsub Upgrade_37.csh 
  230  qstat
  231  cd ../CGPANEL/
  232  ls
  233  ls -l
  234  vi Upgrade_37.csh
  235  wc -l CGPANEL_final_build36.tped CGPANEL_final_build37.tped
  236  vi CGPANEL_final_build36.tped 
  237  head CGPANEL_final.tped|cut -f1-4
  238  head CGPANEL_final.tped|cut -f1-4 -d ' '
  239  head CGPANEL_final_build37.tped|cut -f1-4 -d ' '
  240  head CGPANEL_final_build36.tped|cut -f1-4 -d ' '
  241  grep MESA01 CGPANEL_final.tped
  242  grep rs255 CGPANEL_final.tped
  243  ls
  244  vi Upgrade_37.csh
  245  vi /data4/bsi/bioinf_int/s106381.borawork/naresh_scripts/PAPER/ezimputer/Upgrade_inputmarkers_to_build37_by_DBSNP.pl
  246  perl -c /data4/bsi/bioinf_int/s106381.borawork/naresh_scripts/PAPER/ezimputer/Upgrade_inputmarkers_to_build37_by_DBSNP.pl
  247  vi kk.pl
  248  perl kk.pl rs
  249  perl kk.pl rs1
  250  perl kk.pl rs1234g
  251  vi kk.pl
  252  perl kk.pl rs1234
  253  perl kk.pl rs1234f
  254  perl -c /data4/bsi/bioinf_int/s106381.borawork/naresh_scripts/PAPER/ezimputer/Upgrade_inputmarkers_to_build37_by_DBSNP.pl
  255  vi /data4/bsi/bioinf_int/s106381.borawork/naresh_scripts/PAPER/ezimputer/Upgrade_inputmarkers_to_build37_by_DBSNP.pl
  256  ls
  257  sh Upgrade_37.csh
  258  ls -l 
  259  vi  if($a[1] =~ m/^rs\d+/)
  260  vi CGPANEL_final_build36.tped 
  261  vi /data4/bsi/bioinf_int/s106381.borawork/naresh_scripts/PAPER/ezimputer/Upgrade_inputmarkers_to_build37_by_DBSNP.pl
  262  sh Upgrade_37.csh
  263  ls
  264  ls -l
  265  vi CGPANEL_final_build36.tped 
  266  vi /data4/bsi/bioinf_int/s106381.borawork/naresh_scripts/PAPER/ezimputer/Upgrade_inputmarkers_to_build37_by_DBSNP.pl
  267  sh Upgrade_37.csh
  268  ls -l
  269  vi CGPANEL_final_build36.tped 
  270  vi CGPANEL_final_build37.tped 
  271  gunzip -c ../DB_DIR/b137_SNPChrPosOnRef.bcp.gz |grep 28362304
  272  ls -l ../DB_DIR/b137_SNPChrPosOnRef.bcp.gz 
  273  gunzip -c ../DB_DIR/b137_SNPChrPosOnRef.bcp.gz 
  274  vi /data4/bsi/bioinf_int/s106381.borawork/naresh_scripts/PAPER/ezimputer/Upgrade_inputmarkers_to_build37_by_DBSNP.pl
  275  cd ../DB_DIR/
  276  wget ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606/database/organism_data/b137_SNPChrPosOnRef.bcp.gz
  277  ls
  278  ls -l
  279  mv b137_SNPChrPosOnRef.bcp.gz.1 b137_SNPChrPosOnRef.bcp.gz
  280  vi /data4/bsi/bioinf_int/s106381.borawork/naresh_scripts/PAPER/ezimputer/Upgrade_inputmarkers_to_build37_by_DBSNP.pl
  281  gunzip -c b137_SNPChrPosOnRef.bcp.gz |awk '{if(NF==4)print $0}'|head
  282  gunzip -c b137_SNPChrPosOnRef.bcp.gz |awk '{if(NF>4)print $0}'|head
  283  vi /data4/bsi/bioinf_int/s106381.borawork/naresh_scripts/PAPER/ezimputer/Upgrade_inputmarkers_to_build37_by_DBSNP.pl
  284  perl -c /data4/bsi/bioinf_int/s106381.borawork/naresh_scripts/PAPER/ezimputer/Upgrade_inputmarkers_to_build37_by_DBSNP.pl
  285  cd ..
  286  ls
  287  cd CGPANEL/
  288  ls
  289  perl -c /data4/bsi/bioinf_int/s106381.borawork/naresh_scripts/PAPER/ezimputer/Upgrade_inputmarkers_to_build37_by_DBSNP.pl
  290  perl /data4/bsi/bioinf_int/s106381.borawork/naresh_scripts/PAPER/ezimputer/Upgrade_inputmarkers_to_build37_by_DBSNP.pl
  291  ls
  292  sh Upgrade_37.csh
  293  cd ../
  294  ls
  295  cd DB_DIR/
  296  ls
  297  rm b137_SNPChrPosOnRef.bcp.gz 
  298  cd ..
  299  ls
  300  cd DB_DIR/
  301  ls
  302  vi /data4/bsi/bioinf_int/s106381.borawork/naresh_scripts/PAPER/ezimputer/Upgrade_inputmarkers_to_build37_by_DBSNP.pl
  303  sh Upgrade_37.csh
  304  cd ..
  305  ls
  306  cd CGPANEL/
  307  sh Upgrade_37.csh
  308  ls -l
  309  vi CGPANEL_final_build37.tped 
  310  vi CGPANEL_final_build36.tped 
  311  cd ..
  312  ls
  313  cd EXOME/
  314  ls
  315  cd ../IBC/
  316  ls
  317  ls -l
  318  qsub Upgrade_37.csh
  319  cd ../AFFY/
  320  ls
  321  ls -l
  322  qsub Upgrade_37.csh
  323  history|grep tar
  324  ls -l
  325  qstat
  326  qdel 1099827
  327  qdel 1100130
  328  qdel 1100134
  329  ls
  330  qsub  Upgrade_37.csh
  331  cd ../IBC/
  332  qsub Upgrade_37.csh
  333  qstta
  334  qstat
  335  ls -l
  336  wc -l *build3*tped
  337  cd ..
  338  ls
  339  cd EXOME/
  340  ls
  341  cp ../IBC/Upgrade_37.csh .
  342  pwd
  343  ls
  344  vi Upgrade_37.csh 
  345  qsub Upgrade_37.csh 
  346  ls -l
  347  wc -l *.tped
  348  vi Exome_final_build37_old.tped 
  349  cut -f4 -d ' ' Exome_final_build37_old.tped > k1
  350  gunzip -c ../DB_DIR/b137_SNPChrPosOnRef.bcp.gz |head
  351  cut -f1,4 -d ' ' Exome_final_build37_old.tped |head
  352  cut -f1,4 -d ' ' Exome_final_build37_old.tped >k1
  353  wc -l k1
  354  vi k1
  355  gunzip -c ../DB_DIR/b137_SNPChrPosOnRef.bcp.gz |cut -f2,3 |sed 's/\t/ /g'|head
  356  gunzip -c ../DB_DIR/b137_SNPChrPosOnRef.bcp.gz |cut -f2,3 |sed 's/\t/ /g' > k2
  357  wc -l k1 k2
  358  vi k2
  359  cat k1 k2|sort
  360  cat k1 k2|sort|uniq -d|wc -l
  361  gunzip -c ../DB_DIR/b137_SNPChrPosOnRef.bcp.gz |cut -f2,3 |sed 's/\t/ /g'|sort|uniq>k2
  362  pwd
  363  gunzip -c ../DB_DIR/b137_SNPChrPosOnRef.bcp.gz |cut -f2,3 |sed 's/\t/ /g'|sort|uniq>k2
  364  wc -l k1 k2
  365  cat k1 k2|sort|uniq -d|wc -l
  366  rm k1 k2
  367  ls
  368  vi Exome_final_build37.tped 
  369  grep rs6685064 Exome_final.tped |cut -f1-4 -d ' '
  370  grep rs6685064 Exome_final_build37.tped |cut -f1-4 -d ' '
  371  ls
  372  rm Exome_final_build37_old.tped Exome_final_build37.tped 
  373  rm Upgrade_37.csh.e1100779 Upgrade_37.csh.o1100779
  374  vi Upgrade_37.csh 
  375  vi /data4/bsi/bioinf_int/s106381.borawork/naresh_scripts/PAPER/ezimputer/Upgrade_inputmarkers_to_build37_by_DBSNP.pl
  376  cp /data4/bsi/bioinf_int/s106381.borawork/naresh_scripts/PAPER/ezimputer/Upgrade_inputmarkers_to_build37_by_DBSNP.pl Upgrade_rsids_by_DBSNP.pl 
  377  vi Upgrade_rsids_by_DBSNP.pl 
  378  ls
  379  gunzip -c ../DB_DIR/b137_SNPChrPosOnRef.bcp.gz |cut -f2|head
  380  gunzip -c ../DB_DIR/b137_SNPChrPosOnRef.bcp.gz |cut -f2|sort|uniq
  381  vi perl_update_rsid.pl
  382  gunzip -c  ../DB_DIR/b137_SNPChrPosOnRef.bcp.gz |head
  383  vi perl_update_rsid.pl
  384  perl perl_update_rsid.pl
  385  $pwd
  386  pwd
  387  vi perl_update_rsid.pl
  388  cat perl_update_rsid.pl
  389  ls /data4/bsi/bioinf_ext2/s109990/m081429_mesa/FINAL_MERGING/DB_DIR/b137_SNPChrPosOnRef.bcp.gz /data4/bsi/bioinf_ext2/s109990/m081429_mesa/FINAL_MERGING/EXOME/Exome_final.tped
  390  ls
  391  vi Upgrade_
  392  vi Upgrade_37.csh 
  393  qsub Upgrade_37.csh 
  394  vi Upgrade_37.csh 
  395  cd ..
  396  ls
  397  cd IBC
  398  ls
  399  rm Upgrade_37.csh.e*
  400  rm Upgrade_37.csh.o*
  401  ls
  402  cp IBC_final.tfam IBC_final_build37.tfam
  403  plink --tfile IBC_final_build37 --missing
  404  ls
  405  cd ../AFFY/
  406  ls
  407  rm Upgrade_37.csh.e*
  408  rm Upgrade_37.csh.o*
  409  cp AFFY_final.tfam AFFY_final_build37.tfam
  410  ls
  411  plink --tfile AFFY_final_build37 --missing
  412  ls- l
  413  ls -l
  414  vi AFFY_final_build36.tped 
  415  rm AFFY_final_build36.tped AFFY_final_build37.tfam AFFY_final_build37.tped 
  416  ls /data4/bsi/bioinf_int/s106381.borawork/naresh_scripts/scripts_all/
  417  vi /data4/bsi/bioinf_int/s106381.borawork/naresh_scripts/scripts_all/perl_map_ids.pl 
  418  qstat
  419  ls -l
  420  vi Upgrade_37.csh 
  421  pwd
  422  ls
  423  vi /data4/bsi/bioinf_int/s106381.borawork/naresh_scripts/scripts_all/perl_map_ids.pl
  424  ls /data4/bsi/bioinf_ext1/s113544.pavd_genetics/
  425  ls -l /data4/bsi/bioinf_ext1/s113544.pavd_genetics/
  426  ls -l /data4/bsi/bioinf_int/s106381.borawork/naresh_scripts/scripts_all/
  427  ls /data4/bsi/bioinf_int/s106381.borawork/naresh_scripts/scripts_all/data4_impute_all/
  428  vi /data4/bsi/bioinf_int/s106381.borawork/naresh_scripts/scripts_all/data4_impute_all/perl_updateid.pl 
  429  ls
  430  cp ../EXOME/perl_update_rsid.pl perl_update_affy_ids.pl
  431  ls /data4/bsi/bioinf_int/s106381.borawork/naresh_scripts/
  432  ls
  433  ls /data4/bsi/bioinf_int/s106381.borawork/naresh_scripts/SVN/tcga_dataprocess_boraworkflow/bin/GenomeWideSNP_6.na30.annot.csv 
  434  vi /data4/bsi/bioinf_int/s106381.borawork/naresh_scripts/SVN/tcga_dataprocess_boraworkflow/bin/GenomeWideSNP_6.na30.annot.csv 
  435  vi perl_update_affy_ids.pl 
  436  perl perl_update_affy_ids.pl |head
  437  vi perl_update_affy_ids.pl 
  438  perl perl_update_affy_ids.pl |head
  439  vi perl_update_affy_ids.pl 
  440  ls -l
  441  vi perl_update_affy_ids.pl 
  442  perl perl_update_affy_ids.pl 
  443  ls -l
  444  cut -f2 -d ' ' AFFY_final_rsid.tped |head
  445  cut -f2 -d ' ' AFFY_final.tped |head
  446  vi Upgrade_37.csh 
  447  qsub Upgrade_37.csh 
  448  qstat
  449  qdel 1106212
  450  ls -l
  451  rm Upgrade_37.csh.e1106212 Upgrade_37.csh.o1106212 
  452  vi Upgrade_37.csh
  453  ls  /data4/bsi/bioinf_ext2/s109990/m081429_mesa/FINAL_MERGING/AFFY/AFFY_final_rsid.tped 
  454  qsub Upgrade_37.csh
  455  qstat
  456  vi ../../merge_IBC/nature_prot/imiss-vs-het.Rscript 
  457  ls
  458  ls -l
  459  qstat
  460  ls -l
  461  vi Upgrade_37.csh.e1106213 
  462  vi Upgrade_37.csh
  463  vi /data4/bsi/bioinf_int/s106381.borawork/naresh_scripts/PAPER/ezimputer/Upgrade_inputmarkers_to_build37_by_DBSNP.pl
  464  grep sort /data4/bsi/bioinf_int/s106381.borawork/naresh_scripts/PAPER/ezimputer/*.pl
  465  vi /data4/bsi/bioinf_int/s106381.borawork/naresh_scripts/PAPER/EasyImputer_v2/Upgrade_inputmarkers_to_build37_by_DBSNP.pl 
  466  vi /data4/bsi/bioinf_int/s106381.borawork/naresh_scripts/PAPER/EasyImputer/Upgrade_inputmarkers_to_build37_by_DBSNP.pl 
  467  vi /data4/bsi/bioinf_int/s106381.borawork/naresh_scripts/PAPER/EasyImputer_v2/Upgrade_inputmarkers_to_build37_by_DBSNP.pl 
  468  vi /projects/bsi/gentools/src/Impute2Workflow/Upgrade_inputmarkers_to_build37_by_DBSNP.pl 
  469  vi /data4/bsi/bioinf_int/s106381.borawork/naresh_scripts/PAPER/ezimputer/Upgrade_inputmarkers_to_build37_by_DBSNP.pl 
  470  ls
  471  sh Upgrade_37.csh
  472  vi /data4/bsi/bioinf_int/s106381.borawork/naresh_scripts/PAPER/ezimputer/Upgrade_inputmarkers_to_build37_by_DBSNP.pl 
  473  perl /data4/bsi/bioinf_int/s106381.borawork/naresh_scripts/PAPER/ezimputer/Upgrade_inputmarkers_to_build37_by_DBSNP.pl 
  474  vi /data4/bsi/bioinf_int/s106381.borawork/naresh_scripts/PAPER/ezimputer/Upgrade_inputmarkers_to_build37_by_DBSNP.pl 
  475  perl /data4/bsi/bioinf_int/s106381.borawork/naresh_scripts/PAPER/ezimputer/Upgrade_inputmarkers_to_build37_by_DBSNP.pl -REMAPPED_CURRENT_BUILD ./AFFY_final_rsid.tfam 
  476  perl /data4/bsi/bioinf_int/s106381.borawork/naresh_scripts/PAPER/ezimputer/Upgrade_inputmarkers_to_build37_by_DBSNP.pl -REMAPPED_CURRENT_BUILD $PWD/AFFY_final_rsid.tfam 
  477  vi /data4/bsi/bioinf_int/s106381.borawork/naresh_scripts/PAPER/ezimputer/Upgrade_inputmarkers_to_build37_by_DBSNP.pl 
  478  grep sort /data4/bsi/bioinf_int/s106381.borawork/naresh_scripts/PAPER/ezimputer/Upgrade_inputmarkers_to_build37_by_DBSNP.pl 
  479  ls -l
  480  rm Upgrade_37.csh.e1106213  Upgrade_37.csh.o1106213 
  481  qsub Upgrade_37.csh 
  482  qdel  1107846
  483  qstat
  484  ls
  485  vi /data4/bsi/bioinf_int/s106381.borawork/naresh_scripts/PAPER/ezimputer/Upgrade_inputmarkers_to_build37_by_DBSNP.pl 
  486  qsub Upgrade_37.csh 
  487  history|grep tar
  488  qstat
  489  ls -l
  490  wc -l AFFY_final_rsid_build37.tped 
  491  cut -f1,4 -d ' ' AFFY_final_build37.tped |sort|uniq -d
  492  cut -f1,4 -d ' ' AFFY_final_rsid_build37.tped |sort|uniq -d
  493  cut -f2 -d ' ' AFFY_final_rsid_build37.tped |sort|uniq -d
  494  ls
  495  cp AFFY_final_rsid.tfam AFFY_final_rsid_build37.tam
  496  mv AFFY_final_rsid_build37.tam AFFY_final_rsid_build37.tfam
  497  plink --tfile AFFY_final_rsid_build37 --missing
  498  ls -l
  499  cd ..
  500  ls
  501  ls ./*/*.imiss
  502  ls ./*/*.lmiss
  503  cat ./AFFY/plink.imiss |perl -e 'while(<STDIN>){chomp($_);$_=~s/^ //g;$_=~s/\s+/\t/g;print $_/"\n"}'|head
  504  cat ./AFFY/plink.imiss |perl -e 'while(<STDIN>){chomp($_);$_=~s/^ //g;$_=~s/\s+/\t/g;print $_"\n"}'|head
  505  cat ./AFFY/plink.imiss |perl -e 'while(<STDIN>){chomp($_);$_=~s/^ //g;$_=~s/\s+/\t/g;print $_."\n"}'|head
  506  cat ./AFFY/plink.imiss |perl -e 'while(<STDIN>){chomp($_);$_=~s/^\s+//g;$_=~s/\s+/\t/g;print $_."\n"}'|head
  507  cat ./AFFY/plink.imiss |perl -e 'while(<STDIN>){chomp($_);$_=~s/^\s+//g;$_=~s/\s+/\t/g;print $_."\n"}'|awk '{print NF}'|uniq
  508  cat ./AFFY/plink.imiss |perl -e 'while(<STDIN>){chomp($_);$_=~s/^\s+//g;$_=~s/\s+/\t/g;print $_."\n"}'|awk '{print NF}' >./AFFY/sample.miss
  509  cat ./CGPANEL/plink.imiss |perl -e 'while(<STDIN>){chomp($_);$_=~s/^\s+//g;$_=~s/\s+/\t/g;print $_."\n"}'|awk '{print NF}' >./CGPANEL/sample.miss
  510  cat ./EXOME/plink.imiss |perl -e 'while(<STDIN>){chomp($_);$_=~s/^\s+//g;$_=~s/\s+/\t/g;print $_."\n"}'|awk '{print NF}' >./EXOME/sample.miss
  511  cat ./IBC/plink.imiss |perl -e 'while(<STDIN>){chomp($_);$_=~s/^\s+//g;$_=~s/\s+/\t/g;print $_."\n"}'|awk '{print NF}' >./IBC/sample.imiss
  512  mv ./IBC/sample.imiss ./IBC/sample.miss 
  513  cat ./AFFY/plink.lmiss perl -e 'while(<STDIN>){chomp($_);$_=~s/^\s+//g;$_=~s/\s+/\t/g;print $_."\n"}'|awk '{print NF}' |uniq
  514  cat ./AFFY/plink.lmiss|perl -e 'while(<STDIN>){chomp($_);$_=~s/^\s+//g;$_=~s/\s+/\t/g;print $_."\n"}'|awk '{print NF}' |uniq
  515  cat ./AFFY/plink.lmiss|perl -e 'while(<STDIN>){chomp($_);$_=~s/^\s+//g;$_=~s/\s+/\t/g;print $_."\n"}'|awk '{print NF}' |head
  516  history
  517  history|tail -6
  518  history|tail -16
  519  history|tail -16 > plots.csh
  520  vi plots.csh 
  521  sh plots.csh 
  522  ls -l ./*/sample.miss
  523  ls -l ./*/marker.miss
  524  head /AFFY/sample.miss
  525  head ./AFFY/sample.miss
  526  head ./AFFY/marker.miss
  527  R
  528  ls
  529  ls -l ./*/marker.miss
  530  ls -l ./*/msample.miss
  531  ls -l ./*/sample.miss
  532  vi samplemiss.R 
  533  Rscript samplemiss.R 
  534  vi samplemiss.R 
  535  Rscript samplemiss.R 
  536  cp samplemiss.R markermiss.R
  537  ls -l ./*/marker.miss
  538  vi markermiss.R 
  539  Rscript markermiss.R 
  540  ls
  541  rm markermiss.R 
  542  vi marker_missing.txt 
  543  pwd
  544  ls
  545   gunzip -c /data4/bsi/refdata/genetics/1000Genomes/downloaded_data/release/20110521/impute/ALL_1000G_phase1integrated_v3_impute/ALL_1000G_phase1integrated_v3_chr5_impute.legend.gz |wc -l
  546  ls
  547  cd AFFY/
  548  ls
  549  cd ..
  550  ls
  551  ls ./*/marker.miss
  552  vi ./EXOME/marker.miss 
  553  head ./EXOME/marker.miss 
  554  awk '{if($5 > 0.1)print $0}' ./EXOME/marker.miss |head
  555  awk '{if($5 > 0.1)print $0}' ./EXOME/marker.miss |wc -l
  556  awk '{if($5 > 0.5)print $0}' ./EXOME/marker.miss |wc -l
  557  awk '{if($5 > 0.05)print $0}' ./EXOME/marker.miss |wc -l
  558  ls
  559  vi plots.csh 
  560  vi create_indicator_remove_markers_samples.csh
  561  sh create_indicator_remove_markers_samples.csh
  562  cat create_indicator_remove_markers_samples.csh 
  563  wc -l ./*/remove_markers.txt
  564  wc -l ./*/QC_ind_markers.txt
  565  vi /data4/bsi/bioinf_ext2/s109990/m081429_mesa/FINAL_MERGING/sample_missing.txt
  566  vi /data4/bsi/bioinf_ext2/s109990/m081429_mesa/FINAL_MERGING/marker_missing.txt
  567  vi /data4/bsi/bioinf_ext2/s109990/m081429_mesa/FINAL_MERGING/sample_missing.txt
  568  vi create_indicator_remove_markers_samples.csh
  569  ls -l ./AFFY/sample.miss 
  570  ls -l ./*/sample.miss 
  571  ls  ./*/sample.miss 
  572  head ./AFFY/sample.miss 
  573  vi create_indicator_remove_markers_samples.csh
  574  sh create_indicator_remove_markers_samples.csh
  575  tail -5 create_indicator_remove_markers_samples.csh
  576  wc -l ./*/remove_samples.txtremove_samples.txt
  577  wc -l ./*/remove_samples.txt
  578  ls
  579  ls ./AFFY/
  580  ls -l ./AFFY/
  581  vi ./AFFY/plink.log 
  582  ls
  583  vi create_indicator_remove_markers_samples.csh 
  584  ls ./*/*build37.tfam
  585  ls ./EXOME/
  586  vi ./EXOME/plink.l
  587  vi ./EXOME/plink.log 
  588  vi create_indicator_remove_markers_samples.csh 
  589  sh create_indicator_remove_markers_samples.csh 
  590  ls
  591  vi create_indicator_remove_markers_samples.csh 
  592  ls ./EXOME/remove_markers.txt 
  593  wc -l ./*/remove_markers.txt 
  594  rm ./*/remove_markers.txt 
  595  vi create_indicator_remove_markers_samples.csh 
  596  cd CGPANEL/
  597  ls
  598  plink --bfile CGPANEL_final_build37_markerQC_0_01 --remove remove_samples.txt --make-bed --out temp_CGPANEL_final_build37_markerQC_0_01
  599  wc -l *.fam
  600  wc -l remove_samples.txt 
  601  vi remove_samples.txt 
  602  plink --bfile CGPANEL_final_build37_markerQC_0_01 --keep remove_samples.txt --make-bed --out temp_keep
  603  ls- l
  604  ls -l
  605  vi temp_keep.bim
  606  mv temp_keep.bim temp_keep1.bim
  607  awk '{print $1"\t"$2"\t"$3"\t"$4"\t"$5"\t"$6}' temp_keep1.bim |head
  608  awk '{print $1"\t"$2"\t"$3"\t"$4"\t"0"\t"0}' temp_keep1.bim |head
  609  awk '{print $1"\t"$2"\t"$3"\t"$4"\t"0"\t"0}' temp_keep1.bim > temp_keep.bim 
  610  vi temp_keep.bim 
  611  plink --bfile temp_keep --transpose --recode --out temp_keep
  612  ls -l
  613  vi temp_keep.tped 
  614  rm temp_keep*
  615  rm temp_CGPANEL_final_build37_markerQC_0_01.*
  616  ls
  617  history|tail
  618  history|tail -25
  619  cd ..
  620  ls
  621  vi create_indicator_remove_markers_samples.csh 
  622  sh create_indicator_remove_markers_samples.csh 
  623  wc -l ./*/*.fam
  624  vi create_indicator_remove_markers_samples.csh 
  625  ls -l ./AFFY
  626  vi ./AFFY/AFFY_final_rsid_build37_markerQC_0_01_sampleQC_0_01.log 
  627  vi create_indicator_remove_markers_samples.csh 
  628  ls ./IBC/
  629  ls -l ./IBC/
  630  wc -l ./*/*.fam
  631  vi create_indicator_remove_markers_samples.csh 
  632  awk '{if($6 > 0.1)print $1" "$2}' ./CGPANEL/sample.miss > ./CGPANEL/remove_samples.txt
  633  plink --bfile ./CGPANEL/CGPANEL_final_build37_markerQC_0_01 --remove ./CGPANEL/remove_samples.txt --make-bed --out ./CGPANEL/temp_remove
  634  plink --bfile ./CGPANEL/CGPANEL_final_build37_markerQC_0_01 --keep ./CGPANEL/remove_samples.txt --make-bed --out ./CGPANEL/temp_keep
  635  mv ./CGPANEL/temp_keep.bim ./CGPANEL/temp_keep1.bim
  636  awk '{print $1"\t"$2"\t"$3"\t"$4"\t"0"\t"0}' ./CGPANEL/temp_keep1.bim > ./CGPANEL/temp_keep.bim
  637  plink --bfile ./CGPANEL/temp_remove --bmerge ./CGPANEL/temp_keep.bed ./CGPANEL/temp_keep.bim ./CGPANEL/temp_keep.fam --make-bed --out ./CGPANEL/CGPANEL_final_build37_markerQC_0_01_sampleQC_0_01
  638  rm ./CGPANEL/temp_keep1.bim
  639  rm ./CGPANEL/temp_keep.*
  640  rm ./CGPANEL/temp_remove.*
  641  ls -l ./CGPANEL/
  642  wc -l ./CGPANEL/
  643  wc -l ./CGPANEL/*.fam
  644  vi create_indicator_remove_markers_samples.csh 
  645  sh create_indicator_remove_markers_samples.csh 
  646  ls -l
  647  ls -l ./AFFY/*.fam
  648  ls -l ./IBC/*.fam
  649  ls -l ./CGPANEL/*.fam
  650  ls -l ./EXOME/*.fam
  651  wc -l ./EXOME/Exome_final_updated_rsid_filtered_markerQC_0_01.fam ./EXOME/Exome_final_updated_rsid_filtered_markerQC_0_01_sampleQC_0_01.fam 
  652  vi create_indicator_remove_markers_samples.csh 
  653  ls ./AFFY/
  654  wc -l ./*/remove_samples.txt
  655  vi create_indicator_remove_markers_samples.csh 
  656  awk '{if($6 > 0.1)print $1" "$2}' ./EXOME/sample.miss > ./EXOME/remove_samples.txt
  657  plink --bfile ./EXOME/Exome_final_updated_rsid_filtered_markerQC_0_01 --remove ./EXOME/remove_samples.txt --make-bed --out ./EXOME/temp_remove
  658  plink --bfile ./EXOME/Exome_final_updated_rsid_filtered_markerQC_0_01 --keep ./EXOME/remove_samples.txt --make-bed --out ./EXOME/temp_keep
  659  mv ./EXOME/temp_keep.bim ./EXOME/temp_keep1.bim
  660  awk '{print $1"\t"$2"\t"$3"\t"$4"\t"0"\t"0}' ./EXOME/temp_keep1.bim > ./EXOME/temp_keep.bim
  661  plink --bfile ./EXOME/temp_remove --bmerge ./EXOME/temp_keep.bed ./EXOME/temp_keep.bim ./EXOME/temp_keep.fam --make-bed --out ./EXOME/Exome_final_updated_rsid_filtered_markerQC_0_01_sampleQC_0_01
  662  rm ./EXOME/temp_keep1.bim
  663  rm ./EXOME/temp_keep.*
  664  rm ./EXOME/temp_remove.*
  665  ls -l ./EXOME/
  666  wc -l ./EXOME/*.fam
  667  wc -l ./CGPANEL/*.fam
  668  wc -l ./IBC/*.fam
  669  vi create_indicator_remove_markers_samples.csh 
  670  awk '{if($6 > 0.1)print $1" "$2}' ./IBC/sample.miss > ./IBC/remove_samples.txt
  671  plink --bfile ./IBC/IBC_final_build37_markerQC_0_01 --remove ./IBC/remove_samples.txt --make-bed --out ./IBC/temp_remove
  672  plink --bfile ./IBC/IBC_final_build37_markerQC_0_01 --keep ./IBC/remove_samples.txt --make-bed --out ./IBC/temp_keep
  673  mv ./IBC/temp_keep.bim ./IBC/temp_keep1.bim
  674  awk '{print $1"\t"$2"\t"$3"\t"$4"\t"0"\t"0}' ./IBC/temp_keep1.bim > ./IBC/temp_keep.bim
  675  plink --bfile ./IBC/temp_remove --bmerge ./IBC/temp_keep.bed ./IBC/temp_keep.bim ./IBC/temp_keep.fam --make-bed --out ./IBC/IBC_final_build37_markerQC_0_01_sampleQC_0_01
  676  rm ./IBC/temp_keep1.bim
  677  rm ./IBC/temp_keep.*
  678  rm ./IBC/temp_remove.*
  679  ls -l ./IBC/*.fam
  680  wc -l ./IBC/*
  681  ls -l ./IBC/
  682  ls
  683  vi create_indicator_remove_markers_samples.csh 
  684  awk '{if($6 > 0.1)print $1" "$2}' ./AFFY/sample.miss > ./AFFY/remove_samples.txt
  685  plink --bfile ./AFFY/AFFY_final_rsid_build37_markerQC_0_01 --remove ./AFFY/remove_samples.txt --make-bed --out ./AFFY/temp_remove
  686  plink --bfile ./AFFY/AFFY_final_rsid_build37_markerQC_0_01 --keep ./AFFY/remove_samples.txt --make-bed --out ./AFFY/temp_keep
  687  mv ./AFFY/temp_keep.bim ./AFFY/temp_keep1.bim
  688  awk '{print $1"\t"$2"\t"$3"\t"$4"\t"0"\t"0}' ./AFFY/temp_keep1.bim > ./AFFY/temp_keep.bim
  689  plink --bfile ./AFFY/temp_remove --bmerge ./AFFY/temp_keep.bed ./AFFY/temp_keep.bim ./AFFY/temp_keep.fam --make-bed --out ./AFFY/AFFY_final_rsid_build37_markerQC_0_01_sampleQC_0_01
  690  rm ./AFFY/temp_keep1.bim
  691  rm ./AFFY/temp_keep.*
  692  rm ./AFFY/temp_remove.*
  693  vi create_indicator_remove_markers_samples.csh 
  694  cat ./AFFY/remove_samples.txt
  695  vi create_indicator_remove_markers_samples.csh 
  696  awk '{if($6 > 0.1)print $1" "$2}' ./AFFY/sample.miss
  697  awk '{if($6 > 0.01)print $1" "$2}' ./AFFY/sample.miss
  698  cat /data4/bsi/bioinf_ext2/s109990/m081429_mesa/FINAL_MERGING/sample_missing.txt
  699  ls
  700  ls ./AFFY/
  701  vi ./AFFY/AFFY_final_rsid_build37_markerQC_0_01.fa
  702  vi ./AFFY/AFFY_final_rsid_build37_markerQC_0_01.fam
  703  vi ./CGPANEL/CGPANEL_final_build37_markerQC_0_01_sampleQC_0_01.fam 
  704  vi ./IBC/IBC_final_build37_markerQC_0_01_sampleQC_0_01.fam 
  705  vi ./EXOME/Exome_final_updated_rsid_filtered_markerQC_0_01_sampleQC_0_01
  706  vi ./EXOME/Exome_final_updated_rsid_filtered_markerQC_0_01_sampleQC_0_01.fam 
  707  vi merge.file
  708  plink --bfile ./AFFY/AFFY_final_rsid_build37_markerQC_0_01  --merge-list merge.file --merge-mode 2 --make-bed --out AFFY_EXOME_IBC_CGPANEL_merged
  709  ls
  710  cat merge.file 
  711  plink --bfile ./AFFY/AFFY_final_rsid_build37_markerQC_0_01 --bmerge ./IBC/IBC_final_build37_markerQC_0_01_sampleQC_0_01.bed ./IBC/IBC_final_build37_markerQC_0_01_sampleQC_0_01.bim ./IBC/IBC_final_build37_markerQC_0_01_sampleQC_0_01.fam  --merge-mode 2 --make-bed --out AFFY_IBC_merged
  712  ls
  713  vi AFFY_EXOME_IBC_CGPANEL_merged.missnp 
  714  rm AFFY_EXOME_IBC_CGPANEL_merged.missnp AFFY_EXOME_IBC_CGPANEL_merged.log 
  715  vi AFFY_IBC_merged.missnp 
  716  plink --bfile ./IBC/IBC_final_build37_markerQC_0_01_sampleQC_0_01 --flip AFFY_IBC_merged.missnp --make-bed --out ./IBC/IBC_final_build37_markerQC_0_01_sampleQC_0_01 
  717  ls -l ./IBC/
  718  plink --bfile ./AFFY/AFFY_final_rsid_build37_markerQC_0_01 --bmerge ./IBC/IBC_final_build37_markerQC_0_01_sampleQC_0_01.bed ./IBC/IBC_final_build37_markerQC_0_01_sampleQC_0_01.bim ./IBC/IBC_final_build37_markerQC_0_01_sampleQC_0_01.fam  --merge-mode 2 --make-bed --out AFFY_IBC_merged
  719  ls
  720  vi AFFY_IBC_merged.missnp 
  721  cat AFFY_IBC_merged.missnp 
  722  grep rs9394812 ./AFFY/AFFY_final_rsid_build37_markerQC_0_01.bim 
  723  grep rs9394812 ./IBC/IBC_final_build37_markerQC_0_01_sampleQC_0_01.bim 
  724  plink --bfile ./AFFY/AFFY_final_rsid_build37_markerQC_0_01 --exclude AFFY_IBC_merged.missnp --bmerge ./IBC/IBC_final_build37_markerQC_0_01_sampleQC_0_01.bed ./IBC/IBC_final_build37_markerQC_0_01_sampleQC_0_01.bim ./IBC/IBC_final_build37_markerQC_0_01_sampleQC_0_01.fam  --merge-mode 2 --make-bed --out AFFY_IBC_merged
  725  cat AFFY_IBC_merged.missnp 
  726  plink --bfile ./IBC/IBC_final_build37_markerQC_0_01_sampleQC_0_01 --exclude AFFY_IBC_merged.missnp --make-bed --out ./IBC/IBC_final_build37_markerQC_0_01_sampleQC_0_01_drop 
  727  plink --bfile ./AFFY/AFFY_final_rsid_build37_markerQC_0_01 --exclude AFFY_IBC_merged.missnp --bmerge ./IBC/IBC_final_build37_markerQC_0_01_sampleQC_0_01_drop.bed ./IBC/IBC_final_build37_markerQC_0_01_sampleQC_0_01_drop.bim ./IBC/IBC_final_build37_markerQC_0_01_sampleQC_0_01_drop.fam  --merge-mode 2 --make-bed --out AFFY_IBC_merged
  728  l s-l
  729  ls -l
  730  plink --bfile AFFY_IBC_merged  --bmerge ./CGPANEL/CGPANEL_final_build37_markerQC_0_01.bed ./CGPANEL/CGPANEL_final_build37_markerQC_0_01.bim ./CGPANEL/CGPANEL_final_build37_markerQC_0_01.fam  --merge-mode 2 --make-bed --out AFFY_IBC_merged_custom
  731  ls
  732  cat AFFY_IBC_merged_custom.missnp 
  733  plink --bfile ./CGPANEL/CGPANEL_final_build37_markerQC_0_01 --flip AFFY_IBC_merged_custom.missnp --make-bed --out AFFY_IBC_merged_custom_flip
  734  plink --bfile AFFY_IBC_merged  --bmerge ./CGPANEL/CGPANEL_final_build37_markerQC_0_01_sampleQC_0_01.bed ./CGPANEL/CGPANEL_final_build37_markerQC_0_01_sampleQC_0_01.bim ./CGPANEL/CGPANEL_final_build37_markerQC_0_01_sampleQC_0_01.fam  --merge-mode 2 --make-bed --out AFFY_IBC_merged_custom
  735  wc -l AFFY_IBC_merged_custom.missnp 
  736  plink --bfile ./CGPANEL/CGPANEL_final_build37_markerQC_0_01_sampleQC_0_01  --flip AFFY_IBC_merged_custom.missnp --make-bed --out CGPANEL/CGPANEL_final_build37_markerQC_0_01_sampleQC_0_01_flip
  737  plink --bfile AFFY_IBC_merged  --bmerge ./CGPANEL/CGPANEL_final_build37_markerQC_0_01_sampleQC_0_01_flip.bed ./CGPANEL/CGPANEL_final_build37_markerQC_0_01_sampleQC_0_01_flip.bim ./CGPANEL/CGPANEL_final_build37_markerQC_0_01_sampleQC_0_01_flip.fam  --merge-mode 2 --make-bed --out AFFY_IBC_merged_custom
  738  wc -l AFFY_IBC_merged_custom.missnp 
  739  ls
  740  head AFFY_IBC_merged.missnp 
  741  head AFFY_IBC_merged_custom.missnp 
  742  grep rs1003483 ./CGPANEL/CGPANEL_final_build37_markerQC_0_01_sampleQC_0_01_flip.bim 
  743  grep rs1003483 AFFY_IBC_merged.bim
  744  plink --bfile ./CGPANEL/CGPANEL_final_build37_markerQC_0_01_sampleQC_0_01_flip --exclude --make-bed --out ./CGPANEL/CGPANEL_final_build37_markerQC_0_01_sampleQC_0_01_flip_drop
  745  plink --bfile ./CGPANEL/CGPANEL_final_build37_markerQC_0_01_sampleQC_0_01_flip --exclude --make-bed AFFY_IBC_merged_custom.missnp --out ./CGPANEL/CGPANEL_final_build37_markerQC_0_01_sampleQC_0_01_flip_drop
  746  plink --bfile ./CGPANEL/CGPANEL_final_build37_markerQC_0_01_sampleQC_0_01_flip --exclude AFFY_IBC_merged_custom.missnp --make-bed --out ./CGPANEL/CGPANEL_final_build37_markerQC_0_01_sampleQC_0_01_flip_drop
  747  ls
  748  plink --bfile AFFY_IBC_merged  --bmerge ./CGPANEL/CGPANEL_final_build37_markerQC_0_01_sampleQC_0_01_flip_drop.bed ./CGPANEL/CGPANEL_final_build37_markerQC_0_01_sampleQC_0_01_flip_drop.bim ./CGPANEL/CGPANEL_final_build37_markerQC_0_01_sampleQC_0_01_flip_drop.fam  --merge-mode 2 --make-bed --out AFFY_IBC_merged_custom
  749  ls -l
  750  rm *.hh
  751  ls
  752  rm AFFY_IBC_merged.bed AFFY_IBC_merged.bim AFFY_IBC_merged.fam
  753  cd EXOM
  754  cd EXOME/
  755  ls
  756  vi Upgrade_rsids_by_DBSNP.pl 
  757  vi Exome_final_updated_rsid_filtered_markerQC_0_01.log 
  758  history|grep Upgrade_rsids_by_DBSNP.pl 
  759  history|grep Exome_final_updated_rsid_filtered
  760  plink --tfile Exome_final_updated_rsid_filtered --missing
  761  cd ..
  762  cat ./EXOME/plink.imiss |perl -e 'while(<STDIN>){chomp($_);$_=~s/^\s+//g;$_=~s/\s+/\t/g;print $_."\n"}' >./EXOME/sample.miss
  763  cat ./EXOME/plink.lmiss |perl -e 'while(<STDIN>){chomp($_);$_=~s/^\s+//g;$_=~s/\s+/\t/g;print $_."\n"}' >./EXOME/marker.miss
  764  awk '{if($5 > 0.05)print $0}' ./EXOME/marker.miss > ./EXOME/QC_ind_markers.txt
  765  plink --tfile ./EXOME/Exome_final_updated_rsid_filtered --geno 0.1 --make-bed --out ./EXOME/Exome_final_updated_rsid_filtered_markerQC_0_01
  766  awk '{if($6 > 0.1)print $1" "$2}' ./EXOME/sample.miss > ./EXOME/remove_samples.txt
  767  plink --bfile ./EXOME/Exome_final_updated_rsid_filtered_markerQC_0_01 --remove ./EXOME/remove_samples.txt --make-bed --out ./EXOME/temp_remove
  768  plink --bfile ./EXOME/Exome_final_updated_rsid_filtered_markerQC_0_01 --keep ./EXOME/remove_samples.txt --make-bed --out ./EXOME/temp_keep
  769  mv ./EXOME/temp_keep.bim ./EXOME/temp_keep1.bim
  770  awk '{print $1"\t"$2"\t"$3"\t"$4"\t"0"\t"0}' ./EXOME/temp_keep1.bim > ./EXOME/temp_keep.bim
  771  plink --bfile ./EXOME/temp_remove --bmerge ./EXOME/temp_keep.bed ./EXOME/temp_keep.bim ./EXOME/temp_keep.fam --make-bed --out ./EXOME/Exome_final_updated_rsid_filtered_markerQC_0_01_sampleQC_0_01
  772  rm ./EXOME/temp_keep1.bim
  773  rm ./EXOME/temp_keep.*
  774  rm ./EXOME/temp_remove.*
  775  ls
  776  plink --bile AFFY_IBC_merged_custom --bmerge ./EXOME/Exome_final_updated_rsid_filtered_markerQC_0_01_sampleQC_0_01.bed ./EXOME/Exome_final_updated_rsid_filtered_markerQC_0_01_sampleQC_0_01.bim ./EXOME/Exome_final_updated_rsid_filtered_markerQC_0_01_sampleQC_0_01.fam --merge-mode 2 --make-bed --out  AFFY_IBC_merged_custom_exome
  777  plink --bfile AFFY_IBC_merged_custom --bmerge ./EXOME/Exome_final_updated_rsid_filtered_markerQC_0_01_sampleQC_0_01.bed ./EXOME/Exome_final_updated_rsid_filtered_markerQC_0_01_sampleQC_0_01.bim ./EXOME/Exome_final_updated_rsid_filtered_markerQC_0_01_sampleQC_0_01.fam --merge-mode 2 --make-bed --out  AFFY_IBC_merged_custom_exome
  778  grep rs2070818 ./EXOME/Exome_final_updated_rsid_filtered_markerQC_0_01_sampleQC_0_01.bim
  779  grep rs2070818 AFFY_IBC_merged_custom.bim 
  780  grep rs16990169 ./EXOME/Exome_final_updated_rsid_filtered_markerQC_0_01_sampleQC_0_01.bim
  781  grep rs16990169 AFFY_IBC_merged_custom.bim
  782  grep rs1800291 AFFY_IBC_merged_custom.bim
  783  grep rs1800291 ./EXOME/Exome_final_updated_rsid_filtered_markerQC_0_01_sampleQC_0_01.bim
  784  ls
  785  head AFFY_IBC_merged_custom.missnp 
  786  grep rs1003483 AFFY_IBC_merged_custom.bim 
  787  grep rs1003483 ./EXOME/Exome_final_updated_rsid_filtered_markerQC_0_01_sampleQC_0_01.bim
  788  grep rs10038095 ./EXOME/Exome_final_updated_rsid_filtered_markerQC_0_01_sampleQC_0_01.bim 
  789  ls
  790  head AFFY_IBC_merged_custom_exome.missnp 
  791  grep rs1000022 ./EXOME/Exome_final_updated_rsid_filtered_markerQC_0_01_sampleQC_0_01.bim
  792  grep rs1000022 AFFY_IBC_merged_custom.bim
  793  plink --bfile ./EXOME/Exome_final_updated_rsid_filtered_markerQC_0_01_sampleQC_0_01 --flip AFFY_IBC_merged_custom_exome.missnp --make-bed --out ./EXOME/Exome_final_updated_rsid_filtered_markerQC_0_01_sampleQC_0_01_flip
  794  ls -l
  795  plink --bile AFFY_IBC_merged_custom --bmerge ./EXOME/Exome_final_updated_rsid_filtered_markerQC_0_01_sampleQC_0_01_flip.bed ./EXOME/Exome_final_updated_rsid_filtered_markerQC_0_01_sampleQC_0_01_flip.bim ./EXOME/Exome_final_updated_rsid_filtered_markerQC_0_01_sampleQC_0_01_flip.fam --merge-mode 2 --make-bed --out  AFFY_IBC_merged_custom_exome
  796  plink --bfile AFFY_IBC_merged_custom --bmerge ./EXOME/Exome_final_updated_rsid_filtered_markerQC_0_01_sampleQC_0_01_flip.bed ./EXOME/Exome_final_updated_rsid_filtered_markerQC_0_01_sampleQC_0_01_flip.bim ./EXOME/Exome_final_updated_rsid_filtered_markerQC_0_01_sampleQC_0_01_flip.fam --merge-mode 2 --make-bed --out  AFFY_IBC_merged_custom_exome
  797  head ./EXOME/Exome_final_updated_rsid_filtered_markerQC_0_01_sampleQC_0_01_flip.bim 
  798  mv ./EXOME/Exome_final_updated_rsid_filtered_markerQC_0_01_sampleQC_0_01_flip.bim ./EXOME/Exome_final_updated_rsid_filtered_markerQC_0_01_sampleQC_0_01_flip_1.bim 
  799  awk '{print $1"\t"$2"\t"0"\t"$4"\t"$5"\t"$6}' ./EXOME/Exome_final_updated_rsid_filtered_markerQC_0_01_sampleQC_0_01_flip_1.bim |head
  800   awk '{print $1"\t"$2"\t"0"\t"$4"\t"$5"\t"$6}' ./EXOME/Exome_final_updated_rsid_filtered_markerQC_0_01_sampleQC_0_01_flip_1.bim > ./EXOME/Exome_final_updated_rsid_filtered_markerQC_0_01_sampleQC_0_01_flip.bim
  801  plink --bfile AFFY_IBC_merged_custom --bmerge ./EXOME/Exome_final_updated_rsid_filtered_markerQC_0_01_sampleQC_0_01_flip.bed ./EXOME/Exome_final_updated_rsid_filtered_markerQC_0_01_sampleQC_0_01_flip.bim ./EXOME/Exome_final_updated_rsid_filtered_markerQC_0_01_sampleQC_0_01_flip.fam --merge-mode 2 --make-bed --out  AFFY_IBC_merged_custom_exome
  802  ls -l
  803  wc -l AFFY_IBC_merged_custom_exome.missnp 
  804  plink --bile ./EXOME/Exome_final_updated_rsid_filtered_markerQC_0_01_sampleQC_0_01_flip --exclude AFFY_IBC_merged_custom_exome.missnp --make-bed --out ./EXOME/Exome_final_updated_rsid_filtered_markerQC_0_01_sampleQC_0_01_flip_drop
  805  plink --bfile ./EXOME/Exome_final_updated_rsid_filtered_markerQC_0_01_sampleQC_0_01_flip --exclude AFFY_IBC_merged_custom_exome.missnp --make-bed --out ./EXOME/Exome_final_updated_rsid_filtered_markerQC_0_01_sampleQC_0_01_flip_drop
  806  ls -l
  807  plink --bfile AFFY_IBC_merged_custom --bmerge ./EXOME/Exome_final_updated_rsid_filtered_markerQC_0_01_sampleQC_0_01_flip_drop.bed ./EXOME/Exome_final_updated_rsid_filtered_markerQC_0_01_sampleQC_0_01_flip_drop.bim ./EXOME/Exome_final_updated_rsid_filtered_markerQC_0_01_sampleQC_0_01_flip_drop.fam --merge-mode 2 --transpose --recode --out  AFFY_IBC_merged_custom_exome
  808  ls -l
  809  gzip AFFY_IBC_merged_custom_exome.tped 
  810  ls
  811  vi config_phase_impute 
  812  cat config_phase_impute 
  813  ls /data4/bsi/bioinf_ext2/s109990/m081429_mesa/FINAL_MERGING/AFFY_IBC_merged_custom_exome.tped.gz /data4/bsi/bioinf_ext2/s109990/m081429_mesa/FINAL_MERGING/AFFY_IBC_merged_custom_exome.tfam /data4/bsi/bioinf_ext2/s109990/m081429_mesa/FINAL_MERGING/
  814  ls /data4/bsi/refdata/genetics/1000Genomes/downloaded_data/release/20110521/impute/ALL_1000G_phase1integrated_v3_impute/
  815  vi config_phase_impute 
  816  ls -l /data4/bsi/bioinf_ext2/s109990/m081429_mesa/FINAL_MERGING/TEST
  817  ls -l /data4/bsi/hypertension/s104892.genoa/impute2/jackson/temp3232013/post_logfiles_sungrid/
  818  vi /data4/bsi/hypertension/s104892.genoa/impute2/jackson/temp3232013/post_logfiles_sungrid/ArrayJob_post.csh.e111656.1
  819  vi /data4/bsi/hypertension/s104892.genoa/impute2/jackson/temp3232013/post_logfiles_sungrid/ArrayJob_post.csh.e1116556.1
  820  ls /data4/bsi/hypertension/s104892.genoa/impute2/jackson/temp3232013/1
  821  ls -l /data4/bsi/hypertension/s104892.genoa/impute2/jackson/temp3232013/
  822  ls -l /data4/bsi/hypertension/s104892.genoa/impute2/jackson/temp3232013/1/
  823  ls -l /data4/bsi/hypertension/s104892.genoa/impute2/jackson/temp3232013/2
  824  ls -l /data4/bsi/hypertension/s104892.genoa/impute2/jackson/temp3232013/5
  825  ls -l /data4/bsi/hypertension/s104892.genoa/impute2/jackson/temp3232013/6
  826  ls -l /data4/bsi/hypertension/s104892.genoa/impute2/jackson/temp3232013/12
  827  gunzip -c /data4/bsi/hypertension/s104892.genoa/impute2/jackson/temp3232013/12/beagle_r2.gz |wc -l
  828  gunzip -c /data4/bsi/hypertension/s104892.genoa/impute2/jackson/temp3232013/12/Combined_impute_results_3_prob_ind.gz |wc -l
  829  ls
  830  vi config_phase_impute 
  831  vi Impute_Easy_imputer_test.csh 
  832  qsub Impute_Easy_imputer_test.csh 
  833  ls
  834  rm -rf TEST/
  835  cd temp
  836  ls
  837  cd temp1070516922/
  838  ls
  839  cd ..
  840  ls
  841  vi Impute_Easy_imputer_test.csh.e1129554
  842  rm -rf ./temp/temp1070516922/
  843  rm Impute_Easy_imputer_test.csh.e1129554 Impute_Easy_imputer_test.csh.o1129554 
  844  vi ../mesa6814_protein_race.csv 
  845  pwd
  846  vi ../mesa6814_protein_race.csv 
  847  cut -f4 ../mesa6814_protein_race.csv -d ','|sort|uniq
  848  vi ../mesa6814_protein_race.csv 
  849  ls
  850  vi replace_gender_info.pl
  851  head ../mesa6814_protein_race.csv 
  852  vi replace_gender_info.pl
  853  perl replace_gender_info.pl
  854  vi replace_gender_info.pl
  855  perl replace_gender_info.pl
  856  vi replace_gender_info.pl
  857  perl replace_gender_info.pl
  858  vi replace_gender_info.pl
  859  perl replace_gender_info.pl
  860  ls -l
  861  wc -l *.tfam
  862  vi AFFY_IBC_merged_custom_exome_updated.tfam 
  863  mv AFFY_IBC_merged_custom_exome_updated.tfam AFFY_IBC_merged_custom_exome.tfam 
  864  qsub Impute_Easy_imputer_test.csh 
  865  history > hist
  866  vi hist 
  867  cd EXOME/
  868  ls
  869  cp perl_update_rsid.pl /data4/bsi/bioinf_int/s106381.borawork/naresh_scripts/scripts_all/
  870  cd ..
  871  ls
  872  vi hist 
  873  history|grep tar
  874  cd /data4/bsi/bioinf_ext2/s109990/m081429_mesa/FINAL_MERGING/EXOME
  875  ls
  876  vi Exome_final.tped 
  877  cut -f2 -d ' ' Exome_final.tped |grep -P "^rs|head
  878  cut -f2 -d ' ' Exome_final.tped |grep -P "^rs"|head
  879  cut -f2 -d ' ' Exome_final.tped |grep -P "^rs"|head -2
  880  cut -f2 -d ' ' Exome_final.tped |grep -P "^rs"|wc -l
  881  ls
  882  qstat
  883  vi Exome_final_updated_rsid.tped 
  884  cp Exome_final.tfam Exome_final_updated_rsid.tfam
  885  plink --tfile Exome_final_updated_rsid --missing
  886                                                                                                                                                                                            
  887  vi Exome_final_updated_rsid.tped 
  888  ls
  889  vi perl_update_rsid.pl 
  890  vi Exome_final.tped 
  891  vi perl_update_rsid.pl 
  892  perl perl_update_rsid.pl 
  893  vi Upgrade_37.csh
  894  qsub Upgrade_37.csh
  895  cp perl_update_rsid.pl /data4/bsi/bioinf_int/s106381.borawork/naresh_scripts/scripts_all/
  896  cp ../AFFY/perl_update_affy_ids.pl /data4/bsi/bioinf_int/s106381.borawork/naresh_scripts/scripts_all/
  897  vi ../AFFY/perl_update_affy_ids.pl 
  898  cd ../IBC/
  899  ls
  900  cat Upgrade_37.csh 
  901  cd ../CGPANEL/
  902  ls
  903  cp CGPANEL_final.tfam CGPANEL_final_build37.tfam
  904  plink --tfile CGPANEL_final_build37 --missing
  905  qstat
  906  qstat
  907  ls
  908  ls -l
  909  cd ../EXOME/
  910  ;s
  911  ls
  912  ls -l
  913  plink --tfile Exome_final_updated_rsid --missing
  914  ls -l
  915  perl /data4/bsi/bioinf_int/s106381.borawork/naresh_scripts/PAPER/ezimputer/Check_plink_data_ezimputer.pl 
  916  perl /data4/bsi/bioinf_int/s106381.borawork/naresh_scripts/PAPER/ezimputer/Check_plink_data_ezimputer.pl -INPUT_FILE Exome_final_updated_rsid.tped -OUTPUT_FILE Exome_final_updated_rsid_filtered.tped
  917  ls
  918  perl /data4/bsi/bioinf_int/s106381.borawork/naresh_scripts/PAPER/ezimputer/Check_plink_data_ezimputer.pl -INPUT_FILE Exome_final_updated_rsid -OUTPUT_FILE Exome_final_updated_rsid_filtered
  919  ls -l
  920  plink --tfile Exome_final_updated_rsid_filtered --missing
  921  ls -l
  922  vi plink.imiss 
  923  head plink.imiss 
  924  head plink.lmiss 
  925  cd ..
  926  ls
  927  cd IBC/
  928  ls
  929  cd ../CGPANEL/
  930  ls
  931  vi Upgrade_37.csh
  932  ls -l
  933  sh Upgrade_37.csh
  934  vi Upgrade_37.csh
  935  vi Upgrade_37.csh
  936  sh Upgrade_37.csh
  937  ls -l
  938  vi Upgrade_37.csh
  939  cd /data4/bsi/bioinf_int/s106381.borawork/naresh_scripts/PAPER/ezimputer/
  940  cd ..
  941  ls
  942  vi svn_history 
  943  svn checkout https://ezimputer.googlecode.com/svn/trunk/ ezimputer --username naresh.prodduturi@gmail.com
  944  cd ezimputer
  945  ls
  946  svn update Upgrade_inputmarkers_to_build37_by_DBSNP.pl 
  947  svn commit -m "included temp direcotry"
  948  cd ..
  949  ls
  950  history|grep tar
  951  tar -zcvf ezimputer ezimputer
  952  cd ezimputer
  953  ls
  954  ls -l
  955  cd ..
  956  tar -zcvf ezimputer.tar.gz ezimputer
  957  pwd
  958  vi /projects/bsi/hypertension/s104892.genoa/impute/scripts/config2_impute2
  959  ls /data4/bsi/RandD/Workflow/temp
  960  gunzip -c /data4/bsi/hypertension/s104892.genoa/impute2/jackson/temp3232013/5/Combined_impute_results_3_prob.gz |head -1
  961  gunzip -c /data4/bsi/hypertension/s104892.genoa/impute2/jackson/temp3232013/5/Combined_impute_results_3_prob.gz |tail -1
  962  gunzip -c /data4/bsi/hypertension/s104892.genoa/impute2/jackson/temp3232013/5/
  963  gunzip -c /data4/bsi/hypertension/s104892.genoa/impute2/jackson/temp3232013/5/snps_chr5.haps.gz|grep  175601824 
  964  gunzip -c /data4/bsi/hypertension/s104892.genoa/impute2/jackson/temp3232013/processed_beagle_input.tped.gz |grep  175601824
  965  vi /projects/bsi/gentools/src/Impute2Workflow/Phase_Impute_by_parallel_proc.pl 
  966  ls /projects/bsi/gentools/src/Impute2Workflow/Phase_Impute_by_parallel_proc.pl 
  967  history|grep Exome_final_updated_rsid_filtered
  968  perl /data4/bsi/bioinf_int/s106381.borawork/naresh_scripts/PAPER/ezimputer/Check_plink_data_ezimputer.pl -INPUT_FILE Exome_final_updated_rsid.tped -OUTPUT_FILE Exome_final_updated_rsid_filtered.tped
  969  ls
  970  mv EasyImputer ./old
  971  ls /data2/bsi/RandD/Arraybased_RND/tcga_genotyping/AFFY/BLCA/|wc -l
  972  ls /data2/bsi/RandD/Arraybased_RND/tcga_genotyping/AFFY/UCEC/|wc -l
  973  ls /data2/bsi/RandD/Arraybased_RND/tcga_genotyping/AFFY/LAML/|wc -l
  974  ls /data2/bsi/RandD/Arraybased_RND/tcga_genotyping/AFFY/KIRC/|wc -l
  975  ls /data2/bsi/RandD/Arraybased_RND/tcga_genotyping/AFFY/THRC/|wc -l
  976  ls /data2/bsi/RandD/Arraybased_RND/tcga_genotyping/AFFY/THCA/|wc -l
  977  ls /data2/bsi/RandD/Arraybased_RND/tcga_genotyping/AFFY/ESCA/|wc -l
  978  ls /data2/bsi/RandD/Arraybased_RND/tcga_genotyping/AFFY/DBLC/|wc -l
  979  ls /data2/bsi/RandD/Arraybased_RND/tcga_genotyping/AFFY/DLBC/|wc -l
  980  ls
  981  cd ezimputer
  982  ls
  983  cd ..
  984  ls
  985  vi svn_history 
  986  ls
  987   svn checkout https://ezimputer.googlecode.com/svn/trunk/ ezimputer --username naresh.prodduturi@gmail.com
  988  cd ezimputer
  989  ls
  990  ls -l
  991  svn update Filter_1000genome_reference_by_maf.pl 
  992  svn commit -m 'bug fixed Filter_1000genome_reference_by_maf.pl'
  993  cd ..
  994  ls
  995  history|grep tar
  996  rm ezimputer.tar.gz 
  997  tar -zcvf ezimputer.tar.gz ezimputer/
  998  ls
  999    vi /data4/bsi/bioinf_int/s106381.borawork/naresh_scripts/PAPER/ezimputer/Phase_Impute_by_parallel_proc.pl
 1000  du -m /data2/bsi/RandD/Arraybased_RND
 1001  cd /data4/bsi/RandD/Workflow/temp
 1002  ls
 1003  mkdir Wessime
 1004  mv Wessime/ Wessim
 1005  cd Wessim/
 1006  ls
 1007  git
 1008  git clone git://github.com/numpy/numpy.git numpy
 1009  git://github.com/sak042/Wessim.git
 1010  ls
 1011  cd numpy/
 1012  ls
 1013  vi INSTALL.txt 
 1014  vi README.txt 
 1015  vi release.sh 
 1016  ls -l
 1017  ls
 1018  ls ./tools/
 1019  ls
 1020  cd ..
 1021  ls
 1022  wget http://sourceforge.net/projects/numpy/files/NumPy/1.7.1/numpy-1.7.1.tar.gz/download
 1023  find /projects/bsi/ -name 'numpy'
 1024  vi /projects/bsi/RandD/ngs/summer_project/April/galaxy_dist/eggs/numpy-1.3.0-py2.6-linux-x86_64-ucs2.egg/numpy/README.txt 
 1025  python -c 'import numpy; numpy.test()'
 1026  git clone git://github.com/sak042/Wessim.git Wessim
 1027  ls
 1028  cd Wessim/
 1029  ls
 1030  ls -l
 1031  cd ..
 1032  ls
 1033  cd numpy/
 1034  ls
 1035  vi README.txt 
 1036  python -c 'import numpy; numpy.test()'
 1037  cd ..
 1038  python -c 'import numpy; numpy.test()'
 1039  ls
 1040  ls ./Wessim/
 1041  ls ./Wessim/lib/
 1042  python ./Wessim/Wessim1.py 
 1043  history|grep pysam
 1044  history|grep find
 1045  find /projects/bsi/ -name 'pysam'
 1046  ls -l /projects/bsi/bictools/apps/language/pysam/0.6/pysam
 1047  finger  m078940 
 1048  python ./Wessim/Wessim1.py 
 1049  vi ./Wessim/Wessim1.py 
 1050  python ./Wessim/Wessim1.py 
 1051  vi ./Wessim/Wessim1.py 
 1052  python ./Wessim/Wessim1.py 
 1053  which python
 1054  find /projects/bsi/ -name 'gemsim'
 1055  find /projects/bsi/ -name 'wessim '
 1056  find /projects/bsi/ -name 'wessim'
 1057  ls
 1058  wget https://code.google.com/p/pysam/downloads/detail?name=pysam-0.7.4.tar.gz&can=2&q=
 1059  ls
 1060  ls -l
 1061  rm detail\?name\=pysam-0.7.4.tar.gz 
 1062  wget https://pysam.googlecode.com/files/pysam-0.7.4.tar.gz
 1063  ls
 1064  tar -zxvf pysam-0.7.4.tar.gz 
 1065  ls
 1066  rm pysam-0.7.4
 1067  rm pysam-0.7.4.tar.gz 
 1068  ls
 1069  cd pysam-0.7.4/
 1070  ls
 1071  vi INSTALL 
 1072  python setup.py install
 1073  ls cd ..
 1074  ls
 1075  mkdir library
 1076  ls
 1077  rmdir library/
 1078  mkdir ../library
 1079  pwd
 1080  python setup.py install  --install-dir ../library/
 1081  python setup.py --help
 1082  python setup.py install  
 1083  vi setup.py 
 1084  ls
 1085  vi INSTALL 
 1086  python setup.py install --help
 1087  python setup.py install --install-lib ../library/
 1088  ls -l
 1089  set PYTHONPATH=/data4/bsi/RandD/Workflow/temp/Wessim/pysam-0.7.4/../library/ 
 1090  export $PYTHONPATH
 1091  vi ~/.bash_profile 
 1092  source ~/.bash_profile 
 1093  vi ~/.bash_profile 
 1094  source ~/.bash_profile 
 1095  python setup.py install --install-lib ../library/
 1096  python setup.py install --install-lib /data4/bsi/RandD/Workflow/temp/Wessim/pysam-0.7.4/library
 1097  cd ..
 1098  ls
 1099  ls -l
 1100  chmod 775 library/
 1101  cd pysam-0.7.4/
 1102  python setup.py install --install-lib /data4/bsi/RandD/Workflow/temp/Wessim/pysam-0.7.4/library
 1103  python setup.py install --install-lib /data4/bsi/RandD/Workflow/temp/Wessim/library
 1104  vi ~/.bash_profile 
 1105  source ~/.bash_profile 
 1106  python setup.py install --install-lib /data4/bsi/RandD/Workflow/temp/Wessim/library
 1107  ls
 1108  vi INSTALL 
 1109  pysam
 1110  vi THANKS 
 1111  cd ..
 1112  ls
 1113  cd Wessim/
 1114  ls
 1115  python Wessim1.py 
 1116  ls
 1117  cd ..
 1118  ls
 1119  cd pysam-0.7.4/
 1120  ls
 1121  vi INSTALL 
 1122  python setup.py build
 1123  ls
 1124  vi INSTALL 
 1125  python setup.py install --install-lib /data4/bsi/RandD/Workflow/temp/Wessim/library
 1126  cd ..
 1127  ls
 1128  wget http://pypi.python.org/packages/source/v/virtualenv/virtualenv-1.7.1.2.tar.gz
 1129  ls
 1130  tar -xzf virtualenv-1.7.1.2.tar.gz
 1131  ls
 1132  rm virtualenv-1.7.1.2.tar.gz 
 1133  cd virtualenv-1.7.1.2/
 1134  ls
 1135  which python
 1136  /usr/local/biotools/python/2.7/bin/python2.7 virtualenv.py env
 1137  ls
 1138  env/bin/pip install numpy
 1139  env/bin/pip install pysam
 1140  find /projects/bsi/bictools/ -name 'faToTwoBit'
 1141  ls -l /projects/bsi/bictools/apps/alignment/blat/34/faToTwoBit
 1142  /projects/bsi/bictools/apps/alignment/blat/34/faToTwoBit
 1143  vi ../REMEMBER
 1144  find /projects/bsi/bictools/ -name 'Gemsim'
 1145  cd ..
 1146  ls
 1147  wget http://downloads.sourceforge.net/project/gemsim/GemSIM_v1.6.tar.gz?r=http%3A%2F%2Fsourceforge.net%2Fprojects%2Fgemsim%2F&ts=1366215578&use_mirror=superb-dca2
 1148  ls
 1149  tar -zxvf GemSIM_v1.6.tar.gz 
 1150  ls
 1151* 
 1152  tar -zxvf GemSIM_v1.6.tar.gz 
 1153  rm -rf GemSIM_v1.6.tar.gz 
 1154  ls
 1155  cd GemSIM_v1.6/
 1156  ls
 1157  python GemStats.py 
 1158  cd ..
 1159  ls
 1160  cd Wessim/
 1161  ls
 1162  python Wessim1.py 
 1163  cd ..
 1164  ls
 1165  history > hist
 1166  mv hist Wessim
 1167  ls
 1168  history > Wessim_install.csh
